Genome-wide analysis of tomato NF-Y factors and their role in fruit ripening.

Shan Li,Hongliang Zhu,Yunbo Luo,Ka Li,Daqi Fu,Benzhong Zhu,Zheng Ju,Dongyan Cao

doi:10.1186/s12864-015-2334-2

Abstract

BackgroundFruit ripening is a complex developmental process that depends on a coordinated regulation of numerous genes, including ripening-related transcription factors (TFs), fruit-related microRNAs, DNA methylation and chromatin remodeling. It is known that various TFs, such as MADS-domain, MYB, AP2/ERF and SBP/SPL family proteins play key roles in modulating ripening. However, little attention has been given to members of the large NF-Y TF family in this regard, although genes in this family are known to have important functions in regulating plant growth, development, and abiotic or biotic stress responses.ResultsIn this study, the evolutionary relationship between Arabidopsis thaliana and tomato (Solanum lycopersicum) NF-Y genes was examined to predict similarities in function. Furthermore, through gene expression analysis, 13 tomato NF-Y genes were identified as candidate regulators of fruit ripening. Functional studies involving suppression of NF-Y gene expression using virus induced gene silencing (VIGS) indicated that five NF-Y genes, including two members of the NF-YB subgroup (Solyc06g069310, Solyc07g065500) and three members of the NF-YA subgroup (Solyc01g087240, Solyc08g062210, Solyc11g065700), influence ripening. In addition, subcellular localization analyses using NF-Y proteins fused to a green fluorescent protein (GFP) reporter showed that the three NF-YA proteins accumulated in the nucleus, while the two NF-YB proteins were observed in both the nucleus and cytoplasm.ConclusionsIn this study, we identified tomato NF-Y genes by analyzing the tomato genome sequence using bioinformatics approaches, and characterized their chromosomal distribution, gene structures, phylogenetic relationship and expression patterns. We also examined their biological functions in regulating tomato fruit via VIGS and subcellular localization analyses. The results indicated that five NF-Y transcription factors play roles in tomato fruit ripening. This information provides a platform for further investigation of their biological functions.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2334-2) contains supplementary material, which is available to authorized users.

Highlights

Fruit ripening is a complex developmental process that depends on a coordinated regulation of numerous genes, including ripening-related transcription factors (TFs), fruit-related microRNAs, DNA methylation and chromatin remodeling
While various families of TFs are clearly associated with ripening regulation, there has been no such connection established for the large Nuclear Factor Y (NF-Y) TF family, despite its known functions in regulating plant growth, development, and abiotic or biotic stress responses [4, 36, 57]
NF-Y TFs, which are known as heme activator proteins (HAPs) or CCAAT binding factors (CBFs), can be categorized as NF-YA, NF-YB (HAP3 or CBF-A) and NF-YC (HAP5 or CBF-C) proteins [39], and they have been shown to bind to CCAAT boxes, which are thought to be present in approximately 30% of eukaryotic promoters [6, 47]

Summary

Introduction

Fruit ripening is a complex developmental process that depends on a coordinated regulation of numerous genes, including ripening-related transcription factors (TFs), fruit-related microRNAs, DNA methylation and chromatin remodeling. The regulatory mechanisms underlying these changes, and that coordinate the up- or down-regulation of large numbers of genes, include many ripening-related transcription factors (TFs), fruit-related microRNAs that target some of these TFs, DNA methylation and chromatin remodeling [55]. Silencing of LeHB1, which encodes a tomato putative HD-zip protein, led to delayed ripening and reduced expression LeACO1, a gene that encodes an ACC oxidase, which is a key enzyme in the biosynthesis of the ripening associated hormone ethylene [40] Members of both bHLH and ARF families have been shown to play diverse roles in fruit development and ripening [32, 72]. Upon arrival in the nucleus, a heterotrimer is formed, comprising the NF-YB and NF-YC heterodimer and NF-YA, which can bind to CCAAT boxes in the promoters or other regions of target genes, [17, 26]

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Conclusion